Impact of cover crop termination timing on the soil microbiome of regenerative no‐till cotton in Texas

Abstract

Optimizing cover crop termination timing (CCTT) is crucial for ensuring sustainable cover crop management under regenerative agriculture. This study investigated how early and delayed CCTTs interact with irrigation regimes to affect soil microbiomes, arbuscular mycorrhizal fungi (AMF) dynamics, and the root‐associated fungal biome in cotton roots. Field trials were conducted at two Texas A&M AgriLife Research sites in Lamesa and Chillicothe, TX. Treatments included (i) no cover (NC), ii) cover terminated at 6 weeks (CT6), and (iii) 2 weeks before cotton planting (CT2), each under base (60% ET replacement) and low (<7 cm) irrigation. Root‐associated soil (0–10 cm) and cotton root samples were collected before peak bloom to assess AMF colonization and spore density, phospholipid fatty acid (PLFA) profiles, and root mycobiome using high‐throughput amplicon sequencing. AMF root colonization (%) was significantly higher under CT6 at both sites. Spore density ranged from 4 to 9 g ^{− 1} soil in Lamesa and 5 to 8 g ^{− 1} in Chillicothe, with significantly higher spores under CT2 in Lamesa. No significant effects of CCTT on microbial community composition were observed based on PLFA analysis. However, base irrigation significantly increased the gram‐positive‐to‐gram‐negative bacterial ratio and the saturated‐to‐unsaturated fatty acid ratio, while low irrigation increased the monounsaturated‐to‐polyunsaturated fatty acid ratio. Ascomycota and Basidiomycota were the dominant fungal phyla across CCTT, with significantly higher Basidiomycota abundance under base irrigation at Lamesa. CCTT did not affect fungal alpha and beta diversity indices; however, alpha diversity was significantly greater under base irrigation at Lamesa. Overall, these results suggest that early termination sustains AMF dynamics while avoiding major shifts in the broader microbial community in cotton.